Well, Hanja can also appear inline in otherwise Hangul texts. Vietnamese has a similar issue though their use of an extended Roman alphabet ended up in a slightly different place, Unicode-wise. I don't remember the decision but I believe it might have been at the request of some RoK people.

There might also be an issue if old Hanja-only texts need to be handled differently from Hanzi rendering/processing. That would not surprise me.

Still, I agree it seems pretty weird.